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Co-purification and direct interaction of Ras with caveolin, an integral membrane protein of caveolae microdomains. Detergent-free purification of caveolae microdomains.

Caveolae are plasma membrane specializations that have been implicated in signal transduction. Caveolin, a 21-24-kDa integral membrane protein, is a principal structural component of caveolae membranes in vivo. G protein alpha subunits are concentrated in purified preparations of caveolae membranes, and caveolin interacts directly with multiple G protein alpha subunits, including G(s), G(o), and G(i2). Mutational or pharmacologic activation of G alpha subunits prevents the interaction of caveolin with G proteins, indicating that inactive G alpha subunits preferentially interact with caveolin. Here, we show that caveolin interacts with another well characterized signal transducer, Ras. Using a detergent-free procedure for purification of caveolin-rich membrane domains and a polyhistidine tagged form of caveolin, we find that Ras and other classes of lipid-modified signaling molecules co-fractionate and co-elute with caveolin. The association of Ras with caveolin was further evaluated using two distinct in vitro binding assays. Wild-type H-Ras interacted with glutathione S-transferase (GST)-caveolin fusion proteins but not with GST alone. Using a battery of GST fusion proteins encoding distinct regions of caveolin, Ras binding activity was localized to a 41-amino acid membrane proximal region of the cytosolic N-terminal domain of caveolin. In addition, reconstituted caveolin-rich membranes (prepared with purified recombinant caveolin and purified lipids) interacted with a soluble form of wild-type H-Ras but failed to interact with mutationally activated soluble H-Ras (G12V). Thus, a single amino acid change (G12V) that constitutively activates Ras prevents or destabilizes this interaction. These results clearly indicate that (i) caveolin is sufficient to recruit soluble Ras onto lipid membranes and (ii) membrane-bound caveolin preferentially interacts with inactive Ras proteins. In direct support of these in vitro studies, we also show that recombinant overexpression of caveolin in intact cells is sufficient to functionally recruit a nonfarnesylated mutant of Ras (C186S) onto membranes, overcoming the normal requirement for lipid modification of Ras. Taken together, these observations suggest that caveolin may function as a scaffolding protein to localize or sequester certain caveolin-interacting proteins, such as wild-type Ras, within caveolin-rich microdomains of the plasma membrane.

Animals↗

Kv11.1 (hERG) Protein Interaction Networks Connect Endocytic Trafficking to Polygenic Influences on Cardiac Repolarization.

Polygenic scores (PGS) capture the combined effect of many common genetic variants on quantitative traits and disease risk, yet their functional consequences at the protein level remain poorly defined. Here, we integrated quantitative and interaction proteomics to resolve how polygenic liability for cardiac repolarization manifests in human cells. We studied human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from donors with extreme PGS for QT interval duration, a clinically relevant electrophysiologic trait associated with arrhythmia risk. Global quantitative proteomics revealed increased abundance of mitochondrial proteins in high-PGS cardiomyocytes. To define protein network-level effects on a key repolarizing ion channel, we performed multiplexed affinity purification-mass spectrometry (AP-MS) of Kv11.1. While mitochondrial changes did not directly explain Kv11.1-associated complexes, interactome analysis revealed increased association of Kv11.1 with myosin motor proteins and endosomal recycling machinery in high-PGS cells. These findings suggest altered channel trafficking dynamics of Kv11.1, distinct from the trafficking defects observed in monogenic Kv11.1 variants. Together, these data show that integrating global and interaction proteomics can resolve how polygenic variation reshapes protein networks. Future work using these methods could connect genomic risk to subcellular remodeling and our work provides a generalizable framework to probe the proteomic basis of complex traits. SIGNIFICANCE STATEMENT: Polygenic scores (PGS) predict disease risk, but how biological pathways are influenced by these common variants remains difficult to define. We generated human induced pluripotent stem cells from individuals with extreme high- and low- PGS for QT interval, a key electrocardiographic measure linked to arrhythmia risk. By combining global proteomics and interactomics for a common ion channel involved in regulating the QT interval (Kv11.1) we found potential mechanisms that are influenced by common genetic traits in patients. Our work provides an approach to connect polygenic scores to pathway-level molecular mechanisms in human cells and a general framework for uncovering how complex genetic architecture drives disease-relevant biology.

AP-MS↗

[Interactive 2D/3D image processing, registration and display system].

This paper presents an integrated system for interactive 2D/3D image processing, registration and display. The main image processing algorithm in the system is image filtering, enhancement, adaptive B-snake model, image registration, pseudo color representation and 3D volume rendering. The system provides good visulization interface and image tool.

Humans↗

Functional cortical interaction patterns in visual perception and visuospatial problem solving.

To explore the integration of functional neuronal interactions in human higher cortical functions, we applied multivariate mathematical techniques to regional cerebral blood flow (rCBF) increases induced by mental activity. rCBF was measured using the intravenous xenon-133 clearance technique with 32 bihemispheric detectors in 84 normal volunteers at rest and during both a visuoperceptual accuracy task and a visuospatial problem solving task. Both paradigms activated rCBF in bilateral premotor, motor and postcentral regions. Bilateral prefrontal activation occurred during problem solving but not during the perceptual accuracy task. Partial correlations coefficients and factor analysis identified significant interactions between numerous cortex regions in both tasks. There were highly ordered and integrated patterns of functional interaction patterns between cortex areas subserving elementary subfunctions of complex behavior. Cortical interaction analysis by such techniques is a useful tool to describe the functional anatomy of large-scale neurocognitive networks in the intact human brain. Imaging functional interactions between active cortex areas are complementary to other experimental neurophysiologic methods to explore brain-behavior relationships in health and disease.

Adolescent↗

[Digital teaching archive. Concept, implementation, and experiences in a university setting].

Film-based teaching files require a substantial investment in human, logistic, and financial resources. The combination of computer and network technology facilitates the workflow integration of distributing radiologic teaching cases within an institution (intranet) or via the World Wide Web (Internet). A digital teaching file (DTF) should include the following basic functions: image import from different sources and of different formats, editing of imported images, uniform case classification, quality control (peer review), a controlled access of different user groups (in-house and external), and an efficient retrieval strategy. The portable network graphics image format (PNG) is especially suitable for DTFs because of several features: pixel support, 2D-interlacing, gamma correction, and lossless compression. The American College of Radiology (ACR) "Index for Radiological Diagnoses" is hierarchically organized and thus an ideal classification system for a DTF. Computer-based training (CBT) in radiology is described in numerous publications, from supplementing traditional learning methods to certified education via the Internet. Attractiveness of a CBT application can be increased by integration of graphical and interactive elements but makes workflow integration of daily case input more difficult. Our DTF was built with established Internet instruments and integrated into a heterogeneous PACS/RIS environment. It facilitates a quick transfer (DICOM_Send) of selected images at the time of interpretation to the DTF and access to the DTF application at any time anywhere within the university hospital intranet employing a standard web browser. A DTF is a small but important building block in an institutional strategy of knowledge management.

Computer-Assisted Instruction↗

Generating protein interaction maps from incomplete data: application to fold assignment.

MOTIVATION: We present a framework to generate comprehensive overviews of protein-protein interactions. In the post-genomic view of cellular function, each biological entity is seen in the context of a complex network of interactions. Accordingly, we model functional space by representing protein-protein-interaction data as undirected graphs. We suggest a general approach to generate interaction maps of cellular networks in the presence of huge amounts of fragmented and incomplete data, and to derive representations of large networks which hide clutter while keeping the essential architecture of the interaction space. This is achieved by contracting the graphs according to domain-specific hierarchical classifications. The key concept here is the notion of induced interaction, which allows the integration, comparison and analysis of interaction data from different sources and different organisms at a given level of abstraction. RESULTS: We apply this approach to compute the overlap between the DIP compendium of interaction data and a dataset of yeast two-hybrid experiments. The architecture of this network is scale-free, as frequently seen in biological networks, and this property persists through many levels of abstraction. Connections in the network can be projected downwards from higher levels of abstraction down to the level of individual proteins. As an example, we describe an algorithm for fold assignment by network context. This method currently predicts protein folds at 30% accuracy without any requirement of detectable sequence similarity of the query protein to a protein of known structure. We used this algorithm to compile a list of structural assignments for previously unassigned genes from yeast. Finally we discuss ways forward to use interaction networks for the prediction of novel protein-protein interactions. AVAILABILITY: http://www.ebi.ac.uk/~lappe/FoldPred/.

Algorithms↗

Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations.

The binding to the T cell receptor of wild-type and variant HTLV-1 Tax peptide complexed to the major histocompatibility complex has been investigated by means of molecular dynamics simulations. The binding free energy difference is calculated using the molecular mechanics Poisson-Boltzmann surface area and linear interaction energy methods. These methods extract useful information on the binding energetics from simulations of the physical states of the ligands, which are more computationally expedient than the commonly used thermodynamic integration method. The successful reproduction of the relative binding free energies shows that these methods can be useful for free energy calculations and the rational design of drugs and vaccines.

Animals↗

Cutaneomotor integration in human hand motor areas: somatotopic effect and interaction of afferents.

The aim of this study was to elucidate sensorimotor integration in human hand motor areas, its time course, somatotopy and the interaction of sensory fields arising from two different fingers. We studied the influence of different intensities of electrical digital stimulation of two different fingers on motor-evoked potentials elicited in hand muscles by transcranial magnetic stimulation (TMS). Single conditioning electrical stimuli were applied to the right second (D2) and fifth fingers (D5) individually and also to both fingers (D2+D5) simultaneously in six normal volunteers. Magnetic tests, adjusted to produce a response in the abductor digiti minimi muscle of the right hand, were delivered using a circular and a focal coil. The digital stimuli were delivered to the finger at the sensory threshold (ST), at 3 and 5 times the ST, and over the pain threshold at interstimulus intervals (ISIs) ranging from 10 to 100 ms. In order to define the anatomical level of the sensorimotor interactions, the effect of the digital stimulation on TMS was compared to the effect on transcranial electrical stimulation. When the peripheral stimulation was delivered at the ST a small inhibitory effect was found only when stimulating both fingers. At 3 times the ST we detected a topographic distribution of motor-evoked potential inhibition, which partially disappeared at higher intensity (5 times the ST); two types of convergence effects took place at different ISIs. When conditioning stimuli were painful, somatotopy and convergence were lost. Sensorimotor integration shows somatotopy and interaction of afferents at different sites. The intensity of the conditioning stimulus plays an important role in topography and sensory convergence. The importance of these mechanisms in physiology and physiopathology is discussed.

Afferent Pathways↗

New methods for the investigation of blood-biomaterial interaction.

Quantitative microscopy with integrated image processing is a useful tool for investigation of the interaction of blood components with biomaterials. We have developed new automated measuring devices suitable for simultaneously characterizing biological cells (size, shape, localization, migration, electrophoresis), synthetic particles (electrophoretic fingerprinting), and dialysis membranes (morphology, electric charge). These techniques are useful for the investigation of cell adherence on biomaterials, localization of cells in membrane filters (Chemotaxis), characterization of the protein adsorption on model systems, detection of cytokines (produced after lymphocyte-biomaterial contact), and estimation of morphological properties and charge distribution in dialysis membranes.

Biocompatible Materials↗

[Genetic-evolutionary basis of symbiosis doctrine].

The author presents the current notion of symbiosis as one of the main adaptation of an organism to changeable environment. Symbiosis is considered as a super organism genetic system within which there are different interactions (including mutualism and antagonism). Genetic integration of symbiotic partners can be realized as cross regulation of their genes, exchange of gene products (proteins, RNA), gene amplification and sometimes gene transfer between organisms. On the phenotypic level these processes result in signal interactions, integration of partner metabolic systems and development of symbiotic organs. Co-evolution is considered as an assemblage of micro- and macroevolution processes basing on pre-adaptations and proceeding under influence of different forms of natural selection (individual, frequency-depended and kin selection). Symbiosis can be compared with sexual process since both are the forms of organism integration characterized by different genetic mechanisms and evolutionary consequences. The genome evolution in symbiotic microorganisms can proceed by: 1) simplification of genome in obligate symbiosis (loss of genes that are necessary for independent existence, transfer of some genes to the host organism); 2) complication of genome in facultative symbiosis (increase in genome plasticity, structural and functional differentiation of genome into systems controlling free-living and symbiotic parts of life cycle). Most of symbiotic interactions are correlated to an increase in genetic plasticity of an organism that can lead to evolutionary saltations and origin of new forms of life.

Evolution, Molecular↗

An attempt to integrate the individual-psychological and interactional concepts of the origins of schizophrenia.

Individual-psychological studies (psychoanalytical) and interactional studies (based on family research and family therapy) approach the psychological processes connected with the origins of schizophrenia from different angles. They thus complement each other. Five major propositions are formulated to integrate the psychodynamic concepts dealing with vulnerability to schizophrenia. The integration of family- and individual-centred starting-points has proved to be very useful in developing treatment methods for schizophrenic patients.

Humans↗

The role of early visual cortex in visual integration: a neural model of recurrent interaction.

This paper presents a model on the potential functional roles of the early visual cortex in the primate visual system. Our hypothesis is that early visual areas, such as V1, are important for continual interaction among various higher order visual areas during visual processing. The interaction is mediated by recurrent connections between higher order visual areas and V1, manifested in the long-latency context-sensitive activities often observed in neurophysiological experiments, and is responsible for the re-integration of information analysed by the higher visual areas. Specifically, we considered the case of integrating 'what' and 'where' information from the ventral and dorsal streams. We found that such a cortical architecture provides simple solutions and fresh insights into the problems of attentional routing and visual search. The computational viability of this architecture was tested by simulating a large-scale neural dynamical network.

Attention↗

How we interact with objects: learning from brain lesions.

Motor deficits are the most common outcome of brain damage. Although a large part of such disturbances arises from loss of elementary sensorimotor functions, several syndromes cannot be explained purely on these bases. In this article, we briefly describe higher-order motor impairments, with specific attention to the characteristic ability of the human hand to interact with objects and tools. Disruption of this motor skill at several independent levels is used to outline a comprehensive model, in which various current proposals for a modular organization of hand-object interactions can be integrated. In this model, cortical mechanisms related to object interaction are independent from representations of the semantic features of objects.

Brain Injuries↗

Assessment of carcinogenic hazard of chemical mixtures through analysis of binary chemical interaction data.

Assessment of the potential health hazard of environmental complex chemical mixtures is one of the most difficult and challenging problems in toxicology. In this article, we describe the development of an innovative computerized system for ranking and predicting potential cancer hazard of chemical mixtures. We take into consideration both the additive risk of individual carcinogens present and the projected overall interaction effect of the mixture based on analyzing and integrating the possible interaction effects of all binary pairs of individual constituents of the mixture. Using this system, it can be predicted that a number of mixtures of polycyclic aromatic hydrocarbons should have a carcinogenic risk lower than that calculated by the simple additivity model, whereas the reverse is true for a number of other mixtures. The system can be very useful in hazard ranking and priority setting in dealing with mixture problems such as cleanup of hazardous waste.

Drug Interactions↗

Lipid-mediated interactions between intrinsic membrane proteins: a theoretical study based on integral equations.

This study of lipid-mediated interactions between proteins is based on a theory recently developed by the authors for describing the structure of the hydrocarbon chains in the neighborhood of a protein inclusion embedded in a lipid membrane [Lagüe et al., Farad. Discuss. 111:165-172, 1998]. The theory involves the hypernetted chain integral equation formalism for liquids. The exact lateral density-density response function of the hydrocarbon core, extracted from molecular dynamics simulations of a pure dipalmitoylphosphatidylcholine bilayer based on an atomic model, is used as input. For the sake of simplicity, protein inclusions are modeled as hard repulsive cylinders. Numerical calculations were performed with three cylinder sizes: a small cylinder of 2.5-A radius, corresponding roughly to an aliphatic chain; a medium cylinder of 5-A radius, corresponding to a alpha-helical polyalanine protein; and a large cylinder of 9-A radius, representing a small protein, such as the gramicidin channel. The calculations show that the average hydrocarbon density is perturbed over a distance of 20-25 A from the edge of the cylinder for every cylinder size. The lipid-mediated protein-protein effective interaction is calculated and is shown to be nonmonotonic. In the case of the small and the medium cylinders, the lipid-mediated effective interaction of two identical cylinders is repulsive at an intermediate range but attractive at short range. At contact, there is a free energy of -2k(B)T for the 2.5-A-radius cylinder and -9k(B)T for the 5-A-radius cylinder, indicating that the association of two alpha-helices of both sizes is favored by the lipid matrix. In contrast, the effective interaction is repulsive at all distances in the case of the large cylinder. Results were obtained with two integral equations theories: hypernetted chain and Percus-Yevick. For the two theories, all results are qualitatively identical.

1,2-Dipalmitoylphosphatidylcholine↗

A single amino acid change in the yeast retrotransposon Ty5 abolishes targeting to silent chromatin.

Many retrotransposons and retroviruses are thought to select integration sites through interactions with specific chromosomal proteins. In yeast, the Ty5 retrotransposon integrates preferentially with regions bound by silent chromatin, namely the telomeres and the HMR and HML mating loci. A Ty5 mutant (M3) was identified with an approximately 20-fold decrease in targeted integration as measured by a plasmid-based targeting assay. Often chromosomal insertions generated by M3, none were located at the telomeres or silent mating loci. A single amino acid change at the boundary of integrase and reverse transcriptase is responsible for the mutant phenotype. We predict that this mutation lies within a targeting domain that mediates Ty5 target choice by interacting with a component of silent chromatin.

Amino Acid Sequence↗

Lipid-protein interactions and heterogeneous lipid distribution in membranes.

The specificity of lipid interactions with both integral and peripheral proteins is discussed in terms of the microscopic heterogeneity in lipid distribution to which they give rise. The factors giving rise to macroscopic phase separation, namely hydrophobic mismatch for integral proteins and phase transitions for lipid bilayers, also are considered. Simple thermodynamic or phenomenological models are given for the way in which specific lipid interactions with peripheral or integral proteins may be coupled to intrinsic lipid phase transitions and thus enhance the phase separation or domain formation of the lipid.

Mathematics↗

CTLA4-CD80/CD86 interactions on primary mouse CD4+ T cells integrate signal-strength information to modulate activation with Concanavalin A.

The mechanisms by which concanavalin A (Con A), a lectin, activates T cells are poorly studied. A low dose of Con A is stimulatory for T cells, whereas a high dose of Con A results in suppression of proliferation and enhanced T cell death. The expression and functional roles of costimulatory receptors, CD28 and cytotoxic T-lymphocyte antigen 4 (CTLA4), and their ligands, CD80 and CD86, on primary mouse CD4(+) T cells after activation with different doses of Con A were studied. CTLA4-CD80/CD86 interactions in this T:T cell activation model demonstrate distinct outcomes depending on the dose of Con A. CTLA4-CD80/CD86 interactions inhibit CD4(+) T cell cycling and survival after activation with a suppressive dose of Con A by increasing oxidative stress and decreasing levels of BclX(L). The enhanced CD4(+) T cell death with a suppressive dose of Con A is dependent on excess H(2)O(2) and nitric oxide but is independent of Fas and caspase activity. It is surprising that the increased proliferation of CD4(+) T cells with a suppressive dose of Con A on blocking CTLA4-CD80/CD86 interactions is largely interleukin (IL)-2-independent but is cyclosporine A-sensitive. On activation with a stimulatory dose of Con A, CTLA4-CD80/CD86 interactions enhance T cell activation and survival by reducing the production of reactive oxygen species, increasing IL-2 and BclX(L) levels. Here IL-10 but not transforming growth factor-beta plays a functional role. In summary, CTLA4-CD80/CD86 interactions on T cells integrate signal strength, based on the dose of Con A, to enhance or inhibit primary mouse CD4(+) T cell cycling and survival.

Animals↗